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The U.S. Food and Drug Administration does not perform enough pesticide residue tests — on either imported or domestic foods – to say whether the American food supply is safe, according to federal auditors.

The Government Accountability Office report, which was released Thursday, said FDA is testing less than one-tenth of 1 percent of all imported fruits and vegetables and less than 1 percent of domestic fruits and vegetables. Federal auditors said the agency’s pesticide testing program is not “statistically valid,” making it impossible for it to meet one of its mandates, which is to “determine the national incidence and level of pesticide residues in the foods it regulates.”

The GAO, an investigative arm of Congress, also raised concerns about both the FDA’s and the U.S. Department of Agriculture’s decision not to test for many commonly-used pesticides for which the federal government has set strict residue limits. Auditors were critical of FDA and the USDA for failing to disclose this limitation in their annual reports.

USDA tests for pesticide residue in poultry, meat and processed egg products.

Although FDA and USDA are not legally required to test for specific pesticides, they are responsible for enforcing maximum residue limits that are set by the Environmental Protection Agency. When limits are violated, food products are subject to seizure.

The GAO review of the pesticide program was requested by Rep. Paul Tonko, (D-N.Y.), who said the results concerned him and urged the agencies to follow the recommendations of the federal auditors.

“GAO’s report indicates that the monitoring programs used by FDA and FSIS are falling short of their objectives.  Improvements are needed in pesticide residue monitoring,” Tonko said, adding that both agencies “will need to devote more resources to pesticide residue monitoring to implement GAO’s recommendations.”

Tonko acknowledged that Congress will need to provide the “necessary resources” to the FDA and USDA if they want testing to be expanded.

Although the report did not criticize the USDA for its level of testing – and even noted that testing had risen in recent years – auditors did point out that testing rates were once higher. For example, from 2000 to 2009, the agency reduced the number of domestic and imported samples taken for testing from more than 8,000 annually to less than 1,900. But in 2010 and 2011, those annual samples increased to 2,100.

The GAO credited the department with engaging with “EPA on changes with (USDA’s) monitoring program to better provide EPA with data it needs to assess the risks of pesticides.”

In its response to the GAO, the FDA said it would consider creating a better testing model to ensure outcomes are “statistically significant” but it did not commit to doing so, citing cost concerns. The GAO doesn’t have the authority to order federal agencies to follow their recommendations.

Also, the FDA said it would not follow the GAO’s recommendation to disclose the names of pesticides that the agency fails to test for, because it said users could “more easily circumvent” the testing program if it did.

The USDA, which was also advised to begin disclosing the names of pesticides it does not test for, agreed to do so in its annual report.

The GAO said one of its greatest concerns with the annual reports is that although they indicate that residue levels are low and that violations are rare, auditors are concerned that this provides a false picture since the testing does not include many common pesticides.